Evaluation of cfDNA as an early detection assay for dense tissue breast cancer

por Barbirou, Mouadh, Miller, Amanda A., Gafni, Erik, Mezlini, Amel, Zidi, Asma, Boley, Nathan, Tonellato, Peter J.
Publicado 2022

Genome-guided transcript assembly from integrative analysis of RNA sequence data

por Boley, Nathan, Stoiber, Marcus H., Booth, Benjamin W., Wan, Kenneth H., Hoskins, Roger A., Bickel, Peter J., Celniker, Susan E., Brown, James B.
Publicado 2014

Selective time-dependent changes in activity and cell-specific gene expression in human postmortem brain

por Dachet, Fabien, Brown, James B., Valyi-Nagy, Tibor, Narayan, Kunwar D., Serafini, Anna, Boley, Nathan, Gingeras, Thomas R., Celniker, Susan E., Mohapatra, Gayatry, Loeb, Jeffrey A.
Publicado 2021

Machine learning enables detection of early-stage colorectal cancer by whole-genome sequencing of plasma cell-free DNA

por Wan, Nathan, Weinberg, David, Liu, Tzu-Yu, Niehaus, Katherine, Ariazi, Eric A., Delubac, Daniel, Kannan, Ajay, White, Brandon, Bailey, Mitch, Bertin, Marvin, Boley, Nathan, Bowen, Derek, Cregg, James, Drake, Adam M., Ennis, Riley, Fransen, Signe, Gafni, Erik, Hansen, Loren, Liu, Yaping, Otte, Gabriel L., Pecson, Jennifer, Rice, Brandon, Sanderson, Gabriel E., Sharma, Aarushi, St. John, John, Tang, Catherina, Tzou, Abraham, Young, Leilani, Putcha, Girish, Haque, Imran S.
Publicado 2019

Diversity and dynamics of the Drosophila transcriptome

por Brown, James B., Boley, Nathan, Eisman, Robert, May, Gemma E., Stoiber, Marcus H., Duff, Michael O., Booth, Ben W., Wen, Jiayu, Park, Soo, Suzuki, Ana Maria, Wan, Kenneth H., Yu, Charles, Zhang, Dayu, Carlson, Joseph W., Cherbas, Lucy, Eads, Brian D., Miller, David, Mockaitis, Keithanne, Roberts, Johnny, Davis, Carrie A., Frise, Erwin, Hammonds, Ann S., Olson, Sara, Shenker, Sol, Sturgill, David, Samsonova, Anastasia A., Weiszmann, Richard, Robinson, Garret, Hernandez, Juan, Andrews, Justen, Bickel, Peter J., Carninci, Piero, Cherbas, Peter, Gingeras, Thomas R., Hoskins, Roger A., Kaufman, Thomas C., Lai, Eric C., Oliver, Brian, Perrimon, Norbert, Graveley, Brenton R., Celniker, Susan E.
Publicado 2014

The Developmental Transcriptome of Drosophila melanogaster

por Graveley, Brenton R., Brooks, Angela N., Carlson, Joseph W., Duff, Michael O., Landolin, Jane M., Yang, Li, Artieri, Carlo G., van Baren, Marijke J., Boley, Nathan, Booth, Benjamin W., Brown, James B., Cherbas, Lucy, Davis, Carrie A., Dobin, Alex, Li, Renhua, Lin, Wei, Malone, John H., Mattiuzzo, Nicolas R., Miller, David, Sturgill, David, Tuch, Brian B., Zaleski, Chris, Zhang, Dayu, Blanchette, Marco, Dudoit, Sandrine, Eads, Brian, Green, Richard E., Hammonds, Ann, Jiang, Lichun, Kapranov, Phil, Langton, Laura, Perrimon, Norbert, Sandler, Jeremy E., Wan, Kenneth H., Willingham, Aarron, Zhang, Yu, Zou, Yi, Andrews, Justen, Bickel, Peter J., Brenner, Steven E., Brent, Michael R., Cherbas, Peter, Gingeras, Thomas R., Hoskins, Roger A., Kaufman, Thomas C., Oliver, Brian, Celniker, Susan E.
Publicado 2010

The ENCODE Uniform Analysis Pipelines

por Hitz, Benjamin C., Jin-Wook, Lee, Jolanki, Otto, Kagda, Meenakshi S., Graham, Keenan, Sud, Paul, Gabdank, Idan, Strattan, J. Seth, Sloan, Cricket A., Dreszer, Timothy, Rowe, Laurence D., Podduturi, Nikhil R., Malladi, Venkat S., Chan, Esther T., Davidson, Jean M., Ho, Marcus, Miyasato, Stuart, Simison, Matt, Tanaka, Forrest, Luo, Yunhai, Whaling, Ian, Hong, Eurie L., Lee, Brian T., Sandstrom, Richard, Rynes, Eric, Nelson, Jemma, Nishida, Andrew, Ingersoll, Alyssa, Buckley, Michael, Frerker, Mark, Kim, Daniel S, Boley, Nathan, Trout, Diane, Dobin, Alex, Rahmanian, Sorena, Wyman, Dana, Balderrama-Gutierrez, Gabriela, Reese, Fairlie, Durand, Neva C., Dudchenko, Olga, Weisz, David, Rao, Suhas S. P., Blackburn, Alyssa, Gkountaroulis, Dimos, Sadr, Mahdi, Olshansky, Moshe, Eliaz, Yossi, Nguyen, Dat, Bochkov, Ivan, Shamim, Muhammad Saad, Mahajan, Ragini, Aiden, Erez, Gingeras, Tom, Heath, Simon, Hirst, Martin, Kent, W. James, Kundaje, Anshul, Mortazavi, Ali, Wold, Barbara, Cherry, J. Michael
Publicado 2023

The ENCODE Uniform Analysis Pipelines

por Hitz, Benjamin C., Lee, Jin-Wook, Jolanki, Otto, Kagda, Meenakshi S., Graham, Keenan, Sud, Paul, Gabdank, Idan, Strattan, J. Seth, Sloan, Cricket A., Dreszer, Timothy, Rowe, Laurence D., Podduturi, Nikhil R., Malladi, Venkat S., Chan, Esther T., Davidson, Jean M., Ho, Marcus, Miyasato, Stuart, Simison, Matt, Tanaka, Forrest, Luo, Yunhai, Whaling, Ian, Hong, Eurie L., Lee, Brian T., Sandstrom, Richard, Rynes, Eric, Nelson, Jemma, Nishida, Andrew, Ingersoll, Alyssa, Buckley, Michael, Frerker, Mark, Kim, Daniel S, Boley, Nathan, Trout, Diane, Dobin, Alex, Rahmanian, Sorena, Wyman, Dana, Balderrama-Gutierrez, Gabriela, Reese, Fairlie, Durand, Neva C., Dudchenko, Olga, Weisz, David, Rao, Suhas S. P., Blackburn, Alyssa, Gkountaroulis, Dimos, Sadr, Mahdi, Olshansky, Moshe, Eliaz, Yossi, Nguyen, Dat, Bochkov, Ivan, Shamim, Muhammad Saad, Mahajan, Ragini, Aiden, Erez, Gingeras, Tom, Heath, Simon, Hirst, Martin, Kent, W. James, Kundaje, Anshul, Mortazavi, Ali, Wold, Barbara, Cherry, J. Michael
Publicado 2023

Comparative validation of the D. melanogaster modENCODE transcriptome annotation

por Chen, Zhen-Xia, Sturgill, David, Qu, Jiaxin, Jiang, Huaiyang, Park, Soo, Boley, Nathan, Suzuki, Ana Maria, Fletcher, Anthony R., Plachetzki, David C., FitzGerald, Peter C., Artieri, Carlo G., Atallah, Joel, Barmina, Olga, Brown, James B., Blankenburg, Kerstin P., Clough, Emily, Dasgupta, Abhijit, Gubbala, Sai, Han, Yi, Jayaseelan, Joy C., Kalra, Divya, Kim, Yoo-Ah, Kovar, Christie L., Lee, Sandra L., Li, Mingmei, Malley, James D., Malone, John H., Mathew, Tittu, Mattiuzzo, Nicolas R., Munidasa, Mala, Muzny, Donna M., Ongeri, Fiona, Perales, Lora, Przytycka, Teresa M., Pu, Ling-Ling, Robinson, Garrett, Thornton, Rebecca L., Saada, Nehad, Scherer, Steven E., Smith, Harold E., Vinson, Charles, Warner, Crystal B., Worley, Kim C., Wu, Yuan-Qing, Zou, Xiaoyan, Cherbas, Peter, Kellis, Manolis, Eisen, Michael B., Piano, Fabio, Kionte, Karin, Fitch, David H., Sternberg, Paul W., Cutter, Asher D., Duff, Michael O., Hoskins, Roger A., Graveley, Brenton R., Gibbs, Richard A., Bickel, Peter J., Kopp, Artyom, Carninci, Piero, Celniker, Susan E., Oliver, Brian, Richards, Stephen
Publicado 2014

Comparative Analysis of the Transcriptome across Distant Species

por Gerstein, Mark B., Rozowsky, Joel, Yan, Koon-Kiu, Wang, Daifeng, Cheng, Chao, Brown, James B., Davis, Carrie A, Hillier, LaDeana, Sisu, Cristina, Li, Jingyi Jessica, Pei, Baikang, Harmanci, Arif O., Duff, Michael O., Djebali, Sarah, Alexander, Roger P., Alver, Burak H., Auerbach, Raymond, Bell, Kimberly, Bickel, Peter J., Boeck, Max E., Boley, Nathan P., Booth, Benjamin W., Cherbas, Lucy, Cherbas, Peter, Di, Chao, Dobin, Alex, Drenkow, Jorg, Ewing, Brent, Fang, Gang, Fastuca, Megan, Feingold, Elise A., Frankish, Adam, Gao, Guanjun, Good, Peter J., Guigó, Roderic, Hammonds, Ann, Harrow, Jen, Hoskins, Roger A., Howald, Cédric, Hu, Long, Huang, Haiyan, Hubbard, Tim J. P., Huynh, Chau, Jha, Sonali, Kasper, Dionna, Kato, Masaomi, Kaufman, Thomas C., Kitchen, Robert R., Ladewig, Erik, Lagarde, Julien, Lai, Eric, Leng, Jing, Lu, Zhi, MacCoss, Michael, May, Gemma, McWhirter, Rebecca, Merrihew, Gennifer, Miller, David M., Mortazavi, Ali, Murad, Rabi, Oliver, Brian, Olson, Sara, Park, Peter J., Pazin, Michael J., Perrimon, Norbert, Pervouchine, Dmitri, Reinke, Valerie, Reymond, Alexandre, Robinson, Garrett, Samsonova, Anastasia, Saunders, Gary I., Schlesinger, Felix, Sethi, Anurag, Slack, Frank J., Spencer, William C., Stoiber, Marcus H., Strasbourger, Pnina, Tanzer, Andrea, Thompson, Owen A., Wan, Kenneth H., Wang, Guilin, Wang, Huaien, Watkins, Kathie L., Wen, Jiayu, Wen, Kejia, Xue, Chenghai, Yang, Li, Yip, Kevin, Zaleski, Chris, Zhang, Yan, Zheng, Henry, Brenner, Steven E., Graveley, Brenton R., Celniker, Susan E., Gingeras, Thomas R, Waterston, Robert
Publicado 2014